The cooperative interaction of AOB and comammox clade A drives nitrification and N2O emissions in a long-term organic fertilized paddy soil.

The newly discovered complete ammonia oxidizer (comammox Nitrospira) is able to single-step nitrification capability, and increased our understanding of soil nitrogen cycling. However, the response of comammox and ammonia-oxidizing bacteria (AOB) and archaea (AOA) to long-term fertilization and rhizosphere effects in paddy soils and their relative contribution to the nitrification-derived N 2 O emissions is still unclear. Here, we collected rhizosphere and bulk soils with thirty years of different fertilization strategies, i.e., non-fertilization (CK), chemical N, P, and K application (NPK), and NPK plus pig manure application (NPKM), respectively, to test changes in nitrification potential rate (PNR), N 2 O emission fluxes, abundance of ammonia oxidizers and their significant drivers. The result showed that NPKM significantly increased soil C and N levels, the proportion of soil middle-size particles (40.35–148.00 μm class), and soil PNR, but decreased soil N 2 O emissions, especially in the drying time of paddy (P < 0.05), compared to NPK fertilization. NPKM had the highest values of AOA, AOB, and comammox clade A amoA gene copy numbers (P < 0.05), but clade B was increased by the NPK in the rhizosphere soil. Furthermore, fertilization showed greater effects on ammonia oxidizers (except for clade B) than the rhizosphere effect. Mantel test showed that SOM, TP, pH, NH 4 +, and NO 3 − were main abiotic factors causing the niche separation among ammonia oxidizers. Linear regression analysis and structural equation model (SEM) showed that both PNR and N 2 O emission fluxes were significantly associated with the abundance of AOB and comammox clade A (P < 0.05). Therefore, our results underline the importance of AOB together with comammox clade A in nitrification and N 2 O production in long-term organic fertilized paddy fields, which could provide new ideas for the mitigation of N 2 O emission by adopting organic fertilization scenarios in Chinese paddy fields. [Display omitted] • Organic fertilization significantly increased AOA, AOB, and comammox abundances. • The rhizosphere showed negligible impacts on AOA, AOB and comammox clade A. • SOM, NH 4 +-N, and pH were the main drivers of abundance of AOA, AOB and comammox. • AOB and comammox clade A contributed most to N 2 O fluxes in long-term fertilized paddy fields. [ABSTRACT FROM AUTHOR]